7th Paper 4-Dec, Wednesday PRESENTERS:
Early Class: Dax F-G, Qasim A
Late Class: Keely W, Grant T, Jesus De La O
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Hu, X.; Vujanac, M.; Southall, N.; Stebbins, C. E., Inhibitors of the Yersinia protein tyrosine phosphatase through high throughput and virtual screening approaches. Bioorg Med Chem Lett2013, 23 (4), 1056-62. HuYopHVirtualBioorgMedChemLett2013.pdf
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Hey VDSers,
Here is a link to a VDS class Mendeley account. This website will enable students to access the papers and create bibliographies. You have the option of downloading a desktop version or using the website for journal article access.
The username is vdsclass@gmail.com and the password is the same as usual (not the GDocs one - but the one to get on to the laptops in the lab. p............ ).
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3rd Paper 2-Oct, Wednesday PRESENTERS:
Early Class: Caroline, Imran, Oscar
Late Class: Jason, Ariel
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys 2009, 483 (1), 23-8. Bai, Y.; Watt, B.; Wahome, P.; Mantis, N.; Robertus, J., Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon2010,56 (4), 526-34.
4th Paper 16-Oct , Wednesday PRESENTERS:
Early Class: Aditi, Seo, Jessica (must go at beginning of class)
Late Class: Daniel, Jiaqi
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through
Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and
Steven J.M. Jones J. Med. Chem.2009,52, 2667–2672
30-Oct, Wednesday PRESENTERS:
Early Class: Julia, Manuel
Late Class: Gautam, Jensen, James
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol2009,4 (6), 473-83.
Study Q's: answer these and bring paper copy to class
- No Journal Club Study Q's this week - we will only do in class Group Q's.
6th Paper 20-Nov, Wednesday PRESENTERS:
Early Class: Brandy C, William E.
Late Class: Feng G, Nicole W., D'Ondria P.
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem2007,282 (27), 19905-16.
Start out with a title slide that has the Journal Article name, Journal Name and Authors__ on it.
Put YOUR name on title slide also since you are presenting.
Put the date of the presentation on their as well - and something like 'VDS Journal Club'
Create an introduction that provides a broad perspective for the specific [[#|work]] being presented. For example, if you are presenting a [[#|paper]] on a new protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
Include a picture or image that helps give a visual for the background.
Include any statistics about the disease and its prevalence (this is motivation)
Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any techniques that we are currently using in our lab?
Include graphs and figures from the paper.Use the SNIPPING tool in Windows to get pictures of the graphs, etc. from the paper. However, you will want a few 'original' images of your own. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
Do the results suggest any additional experiments that would be the next.?
Feel free to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
What is the most significant contribution of the specific work to the field in general?
Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
Go through your talk at least once as a practice run
TIPS:
for best contrast and readability - use black text on white background.
Put date on the title slide
When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?
Run a draft of your presentation by Dr. B a few days before you present it.
Upload your presentation before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
Potential Papers:
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis2011,5 (11), e1411.
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem2007,282 (27), 19905-16.
Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol2008, 6 (1), 41-52.
7th Paper
4-Dec, Wednesday
PRESENTERS:
Early Class: Dax F-G, Qasim A
Late Class: Keely W, Grant T, Jesus De La O
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Hu, X.; Vujanac, M.; Southall, N.; Stebbins, C. E., Inhibitors of the Yersinia protein tyrosine phosphatase through high throughput and virtual screening approaches. Bioorg Med Chem Lett 2013, 23 (4), 1056-62.
HuYopHVirtualBioorgMedChemLett2013.pdf
Supplement:
HuYopHVirtualBioorgMedChemLett2013mmc1_SUPPLEMENT.docx
Study Q's: answer these and bring paper copy to class
JournalClubQuestions120413_YopH_StudyQs.doc
*
Hey VDSers,
Here is a link to a VDS class Mendeley account. This website will enable students to access the
papers and create bibliographies. You have the option of downloading a desktop version or using the
website for journal article access.
http://www.mendeley.com/
The username is vdsclass@gmail.com and the password is the same as usual (not the GDocs one - but the one to get on to the laptops in the lab. p............ ).
*
Link to Journal Club Summer 13
COMPLETED PAPERS 2013 Fall:
1st Journal Club Fall 2013
1st Paper
4-Sep, Wednesday
PRESENTERS:
Paper:
Kovac, A.; Konc, J.; Vehar, B.; Bostock, J.; Chopra, I.; Janezic, D.; Gobec, S., Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. J Med Chem 2008, 51 (23), 7442-8.
KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf
Study Q's: answer these and bring paper copy to class
JournalClubQuestions090413_DalaDalaLigase_StudyQs.doc
2nd Paper
18-Sep, Wednesday
PRESENTERS:
Early Class: Anita & Melissa
Late Class: Ashlee, Nicolet
Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. Infect Disord Drug Targets 2009, 9 (3), 327-43.
TomlinsonWatowichDengueVirusInfectiousDisordersDrugTargets2009.pdf
Study Q's: answer these and bring paper copy to class
3rd Paper
2-Oct, Wednesday
PRESENTERS:
Early Class: Caroline, Imran, Oscar
Late Class: Jason, Ariel
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys 2009, 483 (1), 23-8.
Bai, Y.; Watt, B.; Wahome, P.; Mantis, N.; Robertus, J., Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon 2010, 56 (4), 526-34.
Study Q's: answer these and bring paper copy to class
JournalClubQuestions100213_RICIN_StudyQs.doc
4th Paper
16-Oct , Wednesday
PRESENTERS:
Early Class: Aditi, Seo, Jessica (must go at beginning of class)
Late Class: Daniel, Jiaqi
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through
Computational Screening against the Neuraminidase. Jianghong An, Davy C. W. Lee, Anna H.Y. Law, Cindy L.H. Yang, Leo L.M. Poon, Allan S.Y. Lau, and
Steven J.M. Jones J. Med. Chem. 2009, 52, 2667–2672
Study Q's: answer these and bring paper copy to class
JournalClubQuestions101613_INFLUENZA_StudyQs.doc
5th Paper
30-Oct, Wednesday
PRESENTERS:
Early Class: Julia, Manuel
Late Class: Gautam, Jensen, James
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.
Study Q's: answer these and bring paper copy to class
- No Journal Club Study Q's this week - we will only do in class Group Q's.
6th Paper
20-Nov, Wednesday
PRESENTERS:
Early Class: Brandy C, William E.
Late Class: Feng G, Nicole W., D'Ondria P.
paper - use PubMed to download the PDF
If you are not on campus, you can use the UT VPN (Virtual Private Network) to get on the campus network
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
Study Q's: answer these and bring paper copy to class
JournalClubQuestions112013_MtDXR_StudyQs.doc
Guidelines:
- TIPS:
- for best contrast and readability - use black text on white background.
- Put date on the title slide
- When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
- For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?
Run a draft of your presentation by Dr. B a few days before you present it.Upload your presentation before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
Potential Papers:
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis 2011, 5 (11), e1411.Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol 2008, 6 (1), 41-52.